PDBe 6gl1

X-ray diffraction
2.62Å resolution

Function and Biology Details

Reactions catalysed:
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Soluble HLA class I histocompatibility antigen, alpha chain E Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 274 amino acids
Theoretical weight: 31.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P13747 (Residues: 22-295; Coverage: 81%)
Gene names: HLA-6.2, HLA-E, HLAE
Sequence domains:
Beta-2-microglobulin Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Capsid protein p24 Chains: P, Q, R, T
Molecule details ›
Chains: P, Q, R, T
Length: 9 amino acids
Theoretical weight: 1.07 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P04585 (Residues: 275-283; Coverage: 1%)
Gene name: gag-pol

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: C2
Unit cell:
a: 244.82Å b: 48.22Å c: 153.02Å
α: 90° β: 117.38° γ: 90°
R-values:
R R work R free
0.226 0.223 0.273
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided